Next generation quantitative microbiological risk assessment: Refinement of the cold smoked salmon-related listeriosis risk model by integrating genomic data

Fritsch, Lena; Guillier, Laurent; Augustin, Jean-Christophe

doi:10.1016/j.mran.2018.06.003

Cited by 47 publications

(58 citation statements)

References 32 publications

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“…This knowledge is of particular importance for identifying most virulent strains in animals (Dreyer et al., ). At the processing or retail level, clonal complex determination and/or WGS‐typing would also bring a new insight of level of risk for RTE food, as it was recently shown that virulence of some strains is particularly higher than others (Maury et al., ; Fritsch et al., ). Gathering information in an EFSA/ECDC database on WGS characterisation of L .…”

Section: Listeriamentioning

confidence: 99%

The European Union One Health 2018 Zoonoses Report

2019

EFS2

589

325

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Section: Listeriamentioning

confidence: 99%

The European Union One Health 2018 Zoonoses Report

2019

EFS2

589

325

View full text Add to dashboard Cite

show abstract

“…In the study by Fritsch et al. (), each of three classes of L. monocytogenes according to their virulence potential was associated with a different dose–response model. The risk assessment showed that uncommon high virulent strains were responsible for the majority of human cases.…”

Section: Assessmentmentioning

confidence: 99%

“…Some studies have already succeeded in the use of WGS for the investigation of genes associated with virulence and the improvement of hazard characterisation, especially with listeriosis. In the study by Fritsch et al (2018), each of three classes of L. monocytogenes according to their virulence potential was associated with a different dose-response model. The risk assessment showed that uncommon high virulent strains were responsible for the majority of human cases.…”

Section: Hazard Characterisationmentioning

confidence: 99%

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2019

EFS2

104

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This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and sourceattribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogenhost interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGSbased genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

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“…To date, all L. monocytogenes isolates are considered to be equally virulent by governmental and international food safety authorities such as the European Food Safety Authority in the European Union and the Food and Drug Administration in the United States. However, it is contradicted by accumulating evidence (11,13). The virulence of L. monocytogenes is determined by its capacity to circumvent innate host barriers such as microbiota (14,15) and its ability to hijack host cell functions during its intracellular life cycle (5,16).…”

mentioning

confidence: 99%

Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella

Lee

Garmyn

Gal

et al. 2019

Appl Environ Microbiol

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As for many opportunistic pathogens, the virulence potential of Listeria monocytogenes is highly heterogeneous between isolates and correlated, to some extent, with phylogeny and gene repertoires. In sharp contrast with copious data on intraspecies genome diversity, little is known about transcriptome diversity despite the role of complex genetic regulation in pathogenicity. The current study implemented RNA sequencing to characterize the transcriptome profiles of 33 isolates under optimal in vitro growth conditions. Transcript levels of conserved single-copy genes were comprehensively explored from several perspectives, including phylogeny, in silico-predicted virulence category based on epidemiological multilocus sequence typing (MLST) data, and in vivo virulence phenotype assessed in Galleria mellonella. Comparing baseline transcriptomes between isolates was intrinsically more complex than standard genome comparison because of the inherent plasticity of gene expression in response to environmental conditions. We show that the relevance of correlation analyses and their statistical power can be enhanced by using principal-component analysis to remove the first level of irrelevant, highly coordinated changes linked to growth phase. Our results highlight the major contribution of transcription factors with key roles in virulence to the diversity of transcriptomes. Divergence in the basal transcript levels of a substantial fraction of the transcriptome was observed between lineages I and II, echoing previously reported epidemiological differences. Correlation analysis with in vivo virulence identified numerous sugar metabolism-related genes, suggesting that specific pathways might play roles in the onset of infection in G. mellonella. IMPORTANCE Listeria monocytogenes is a multifaceted bacterium able to proliferate in a wide range of environments from soil to mammalian host cells. The accumulated genomic data underscore the contribution of intraspecies variations in gene repertoire to differential adaptation strategies between strains, including infection and stress resistance. It seems very likely that the fine-tuning of the transcriptional regulatory network is also a key component of the phenotypic diversity, albeit more difficult to investigate than genome content. Some studies reported incongruity in the basal transcriptome between isolates, suggesting a putative relationship with phenotypes, but small isolate numbers hampered proper correlation analyses with respect to their characteristics. The present study is the embodiment of the promising approach that consists of analyzing correlations between transcriptomes and various isolate characteristics. Statistically significant correlations were found with phylogenetic groups, epidemiological evidence of virulence potential, and virulence in Galleria mellonella larvae used as an in vivo model.

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Next generation quantitative microbiological risk assessment: Refinement of the cold smoked salmon-related listeriosis risk model by integrating genomic data

Cited by 47 publications

References 32 publications

The European Union One Health 2018 Zoonoses Report

The European Union One Health 2018 Zoonoses Report

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella

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